Merge pull request #1076 from INCATools/update-base-system

Upgrade base system to Ubuntu 24.04

CHANGELOG.md

@@ -12,6 +12,7 @@ For more detailed changes see:
 ## New and updated tooling
 
 - New [ROBOT Version 1.9.6](https://github.com/ontodev/robot/releases/tag/v1.9.6). This came with a great number of updates and upgrades, see release notes.
+- J2cli, a command-line tool to process Jinja2 templates, has been replaced by [Jinjanator](https://github.com/kpfleming/jinjanator). If your custom workflows invoke the `j2` tool, you will need to update them to use `jinjanate` instead.
 
 ## New configuration options
 

Dockerfile

@@ -40,9 +40,11 @@ RUN apt-get update && DEBIAN_FRONTEND="noninteractive" apt-get install -y --no-i
     xlsx2csv \
     gh \
     nodejs \
+    npm \
     graphviz \
     python3-psycopg2 \
-    swi-prolog
+    swi-prolog \
+    libpcre3
 
 # Install run-time dependencies for Soufflé.
 RUN DEBIAN_FRONTEND="noninteractive" apt-get install -y --no-install-recommends \
@@ -95,7 +97,7 @@ COPY scripts/obodash /tools
 RUN chmod +x /tools/obodash && \
     git clone --depth 1 https://github.com/OBOFoundry/OBO-Dashboard.git && \
     cd OBO-Dashboard && \
-    python3 -m pip install -r requirements.txt && \
+    python3 -m pip install -r requirements.txt --break-system-packages && \
     echo " " >> Makefile && \
     echo "build/robot.jar:" >> Makefile && \
     echo "	echo 'skipped ROBOT jar download.....' && touch \$@" >> Makefile && \

Makefile

@@ -35,6 +35,7 @@ test_odklite_programs:
 	@./tests/test-program.sh DOSDP-TOOLS dosdp-tools -v
 	@./tests/test-program.sh OWLTOOLS owltools --version
 	@./tests/test-program.sh AMMONITE sh amm --help
+	@./tests/test-program.sh JINJANATOR jinjanate --version
 	@./tests/test-program.sh ODK odk.py
 
 test_odkfull_programs: test_odklite_programs
@@ -168,7 +169,7 @@ publish-multiarch-dev:
 		.
 
 constraints.txt: requirements.txt.full
-	docker run -v $$PWD:/work -w /work --rm -ti obolibrary/odkbuild:latest /work/update-constraints.sh
+	docker run -v $$PWD:/work -w /work --rm -ti obolibrary/odkbuild:latest /work/update-constraints.sh --install-virtualenv
 
 clean-tests:
 	rm -rf target/*

constraints.txt

@@ -12,13 +12,12 @@ async-lru==2.0.4
 attrs==23.2.0
 Babel==2.15.0
 babelon==0.2.9
-backports.tarfile==1.2.0
 bcp47==0.1.0
 beautifulsoup4==4.12.3
 bidict==0.23.1
 bleach==6.1.0
-bmt==1.4.3
-cachetools==5.3.3
+bmt==1.4.4
+cachetools==5.4.0
 cattrs==23.2.3
 certifi==2024.7.4
 cffi==1.16.0
@@ -32,8 +31,8 @@ colorama==0.4.6
 comm==0.2.2
 commonmark==0.9.1
 contourpy==1.2.1
-cryptography==42.0.8
-curies==0.7.9
+cryptography==43.0.0
+curies==0.7.10
 cycler==0.12.1
 dacite==1.8.1
 daff==1.3.46
@@ -49,26 +48,25 @@ diskcache==5.6.3
 distlib==0.3.8
 distro==1.9.0
 docker==6.1.3
-docutils==0.18.1
+docutils==0.21.2
 dosdp==0.1.10.dev1
 EditorConfig==0.12.4
 et-xmlfile==1.1.0
 eutils==0.6.0
-exceptiongroup==1.2.1
 executing==2.0.1
 fastjsonschema==2.20.0
 fastobo==0.12.3
 filelock==3.15.4
-fonttools==4.53.0
+fonttools==4.53.1
 fqdn==1.5.1
 funowl==0.2.3
 ghp-import==2.1.0
 google==3.0.0
 google-api-core==2.19.1
-google-api-python-client==2.136.0
-google-auth==2.31.0
+google-api-python-client==2.138.0
+google-auth==2.32.0
 google-auth-httplib2==0.2.0
-google-auth-oauthlib==1.2.0
+google-auth-oauthlib==1.2.1
 googleapis-common-protos==1.63.2
 graphviz==0.20.3
 greenlet==3.0.3
@@ -82,7 +80,7 @@ httpx==0.27.0
 idna==3.7
 ijson==3.3.0
 imagesize==1.4.1
-importlib_metadata==8.0.0
+importlib_metadata==8.2.0
 importlib_resources==6.4.0
 inflection==0.5.1
 iniconfig==2.0.0
@@ -91,13 +89,14 @@ ipython==8.26.0
 ipywidgets==8.1.3
 isodate==0.6.1
 isoduration==20.11.0
-j2cli==0.3.10
 jaraco.classes==3.4.0
 jaraco.context==5.3.0
 jaraco.functools==4.0.1
 jedi==0.19.1
 jeepney==0.8.0
 Jinja2==3.1.4
+jinjanator==24.2.0
+jinjanator-plugins==24.1.0
 jsbeautifier==1.15.1
 jsobject==0.10.2
 json-flattener==0.1.9
@@ -110,7 +109,7 @@ jsonpath-ng==1.6.1
 jsonpath-rw==1.4.0
 jsonpickle==3.2.2
 jsonpointer==3.0.0
-jsonschema==4.22.0
+jsonschema==4.23.0
 jsonschema-specifications==2023.12.1
 jsonschema2md==1.1.0
 jsonstreams==0.6.0
@@ -120,16 +119,16 @@ jupyter-events==0.10.0
 jupyter-lsp==2.2.5
 jupyter_client==8.6.2
 jupyter_core==5.7.2
-jupyter_server==2.14.1
+jupyter_server==2.14.2
 jupyter_server_terminals==0.5.3
-jupyterlab==4.2.3
+jupyterlab==4.2.4
 jupyterlab_pygments==0.3.0
-jupyterlab_server==2.27.2
+jupyterlab_server==2.27.3
 jupyterlab_widgets==3.0.11
 keyring==25.2.1
 kgcl-rdflib==0.5.0
 kgcl_schema==0.6.8
-kgx==2.4.0
+kgx==2.4.2
 kiwisolver==1.4.5
 lark==1.1.9
 lightrdf==0.4.0
@@ -145,39 +144,39 @@ MarkupSafe==2.1.5
 marshmallow==3.21.3
 matplotlib==3.9.1
 matplotlib-inline==0.1.7
-matplotlib-venn==0.11.10
+matplotlib-venn==1.0.0
 mdurl==0.1.2
 mergedeep==1.3.4
 mistune==3.0.2
 mkdocs==1.6.0
 mkdocs-get-deps==0.2.0
-mkdocs-material==9.5.28
+mkdocs-material==9.5.30
 mkdocs-material-extensions==1.3.1
 mkdocs-mermaid2-plugin==1.1.1
 mkdocs-table-reader-plugin==2.2.2
 more-click==0.1.2
 more-itertools==10.3.0
-mypy==1.10.1
+mypy==1.11.0
 mypy-extensions==1.0.0
 nbclient==0.10.0
 nbconvert==7.16.4
 nbformat==5.10.4
 ndex2==3.9.0
-neo4j==4.4.12
+neo4j==5.23.0
 nest-asyncio==1.6.0
 networkx==3.3
-nh3==0.2.17
+nh3==0.2.18
 notebook==7.2.1
 notebook_shim==0.2.4
 numpy==1.26.4
-oaklib==0.6.11
+oaklib==0.6.12
 oauthlib==3.2.2
 ols-client==0.1.4
-ontobio==2.9.1
+ontobio==2.9.3
 ontodev-cogs==0.3.3
 ontodev-gizmos==0.3.2
 ontoportal-client==0.0.4
-openai==1.35.10
+openai==1.37.1
 openpyxl==3.1.5
 ordered-set==4.1.0
 overrides==7.7.0
@@ -193,11 +192,11 @@ pexpect==4.9.0
 pillow==10.4.0
 pkginfo==1.10.0
 platformdirs==4.2.2
-plotly==5.22.0
+plotly==5.23.0
 pluggy==1.5.0
 ply==3.11
 prefixcommons==0.1.12
-prefixmaps==0.2.4
+prefixmaps==0.2.5
 prologterms==0.0.6
 prometheus_client==0.20.0
 prompt_toolkit==3.0.47
@@ -206,7 +205,7 @@ proto-plus==1.24.0
 protobuf==5.27.2
 psutil==6.0.0
 ptyprocess==0.7.0
-pure-eval==0.2.2
+pure_eval==0.2.3
 pyarrow==15.0.2
 pyasn1==0.6.0
 pyasn1_modules==0.4.0
@@ -218,7 +217,7 @@ PyGithub==2.3.0
 Pygments==2.18.0
 PyJSG==0.11.10
 PyJWT==2.8.0
-pymdown-extensions==10.8.1
+pymdown-extensions==10.9
 PyNaCl==1.5.0
 pyparsing==2.4.7
 pyproject-api==1.7.1
@@ -227,7 +226,7 @@ PyShExC==0.9.1
 pysolr==3.9.0
 pyspellchecker==0.8.1
 pystow==0.5.4
-pytest==8.2.2
+pytest==8.3.2
 pytest-logging==2015.11.4
 python-dateutil==2.9.0.post0
 python-dotenv==1.0.1
@@ -244,10 +243,10 @@ ratelimit==2.2.1
 rdflib==7.0.0
 rdflib-jsonld==0.6.1
 rdflib-shim==1.0.3
-readme_renderer==43.0
+readme_renderer==44.0
 recommonmark==0.7.1
 referencing==0.35.1
-regex==2024.5.15
+regex==2024.7.24
 requests==2.32.3
 requests-cache==1.2.1
 requests-oauthlib==2.0.0
@@ -257,14 +256,14 @@ rfc3986==2.0.0
 rfc3986-validator==0.1.1
 rfc3987==1.3.8
 rich==13.7.1
-rpds-py==0.18.1
+rpds-py==0.19.1
 rsa==4.9
 ruamel.yaml==0.18.6
 ruamel.yaml.clib==0.2.8
 scipy==1.14.0
 seaborn==0.13.2
 SecretStorage==3.3.3
-semsimian==0.2.16
+semsimian==0.2.17
 semsql==0.3.3
 Send2Trash==1.8.3
 ShExJSG==0.8.2
@@ -275,29 +274,28 @@ sortedcontainers==2.4.0
 soupsieve==2.5
 sparqlslurper==0.5.1
 SPARQLWrapper==2.0.0
-Sphinx==7.3.7
-sphinxcontrib-applehelp==1.0.8
-sphinxcontrib-devhelp==1.0.6
-sphinxcontrib-htmlhelp==2.0.5
+Sphinx==7.4.7
+sphinxcontrib-applehelp==2.0.0
+sphinxcontrib-devhelp==2.0.0
+sphinxcontrib-htmlhelp==2.1.0
 sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.7
-sphinxcontrib-serializinghtml==1.1.10
+sphinxcontrib-qthelp==2.0.0
+sphinxcontrib-serializinghtml==2.0.0
 SQLAlchemy==2.0.31
 SQLAlchemy-Utils==0.38.3
 sqlite-fts4==1.0.3
 sqlite-migrate==0.1b0
-sqlite-utils==3.36
+sqlite-utils==3.37
 sssom==0.4.11
 sssom-schema==0.15.2
 stack-data==0.6.3
 stringcase==1.2.0
 tabulate==0.9.0
-tenacity==8.4.2
+tenacity==9.0.0
 termcolor==2.4.0
 terminado==0.18.1
 terminaltables==3.1.10
 tinycss2==1.3.0
-tomli==2.0.1
 tornado==6.4.1
 tox==4.16.0
 tqdm==4.66.4

docker/builder/Dockerfile

@@ -3,7 +3,7 @@
 # (typically because pre-compiled binaries don't exist for arm64) and
 # we don't want to build directly on the final image (to avoid
 # cluttering the image with build-time dependencies).
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 WORKDIR /build
 
 # Software versions
@@ -27,8 +27,7 @@ RUN apt-get update && \
         rustc \
         cargo \
         python3-dev \
-        python3-pip \
-        python3-virtualenv
+        python3-pip
 
 # Build the Python packages.
 # On x86_64, most if not all of these packages should be available as
@@ -41,19 +40,22 @@ RUN apt-get update && \
 COPY requirements.txt.full /build/requirements.txt
 COPY requirements.txt.lite /build/requirements.txt.lite
 COPY constraints.txt /build/constraints.txt
+RUN echo "setuptools<72" > /build/pip-constraints.txt
 # First the packages needed by the odklite image.
-RUN python3 -m pip install \
+RUN PIP_CONSTRAINT=/build/pip-constraints.txt python3 -m pip install \
         -r /build/requirements.txt.lite \
         -c /build/constraints.txt \
+        --no-warn-script-location \
         --root /staging/lite
 # Then those needed by the odkfull image.
 # After installing those packages, we forcibly remove from the odkfull
 # staging tree any file already present in the odklite staging tree
 # (caused by packages installed in both trees) to avoid needlessly
 # increasing the size of the odkfull image.
-RUN python3 -m pip install \
+RUN PIP_CONSTRAINT=/build/pip-constraints.txt python3 -m pip install \
         -c /build/constraints.txt \
         -r /build/requirements.txt \
+        --no-warn-script-location \
         --root /staging/full && \
         cd /staging/lite && \
         find . -type f | while read f ; do rm -f /staging/full/$f ; done && \

docker/odklite/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 LABEL maintainer="[email protected]"
 
 ENV ROBOT_VERSION=1.9.6

docker/robot/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 LABEL maintainer="[email protected]" 
 
 WORKDIR /tools